Mn3Ge, a typical member of the Heusler family, has a high spin polarization and large spin Hall angle, making it a potential material for spintronic devices. Regarded as a topological Weyl semi-metal, Mn3Ge could be applied in topological spintronics owing to its special Fermi-arc-type surface states and various spin transport properties. In this study, we grew high-quality perpendicularly magnetized Mn3Gefilms through magnetron sputtering. X-ray diffraction (XRD) showed that hexagonal antiferromagnetic Mn3Ge was mixed with tetragonal ferromagnetic Mn3Ge. Thickness-dependent double-phase Mn3Ge films with large magnetic anisotropy and robust anomalous Hall effect (AHE) were obtained. The triangular spin structure of hexagonal Mn3Ge enhances the AHE; however, it shrinks the coercivity of the tetragonal ferromagnetic property. This manipulation of coexisting multi-phases comes from the strain of the substrate during growth, achieved by controlling the film thickness. Structural, magnetic, and transport measurements demonstrated stress modulation of the defect pinning, magnetic anisotropy, and spin transport properties. The coexistence of antiferromagnetic and ferromagnetic Mn3Ge provides the possibility of a new generation of Mn3X-based devices for applications in spin-torque memories.